pagurus's Introduction

pagurus

Used for getting the information from a running job based on its pid using psutil.

Install

Availible on PyPi and easily installed in your enviroment.

pip install pagurus

Options

usage: pagurus [-h] [-o OUTFILE] [-p PATH] [-d] [-r RATE] [-u USER] [-noh] [-mv] [-l ROLLING] [--json] [--envvar ENVVAR]

options:
  -h, --help            show this help message and exit
  -o OUTFILE, --outfile OUTFILE
                        File name for csv.
  -p PATH, --path PATH  Path to put csv file.
  -d, --debug           Run with debugging info.
  -r RATE, --rate RATE  Polling rate for process.
  -u USER, --user USER  Username to get stats for.
  -noh, --no-header     Turn off writting the header.
  -mv, --move           Moves file from 'running' to 'done' directories
  -l ROLLING, --rolling ROLLING
                        Time to roll file over to number to file name in ~minutes.
  --json                Output JSON strings instead of CSV lines
  --envvar ENVVAR       add environment var to output (can be specified multiple times)

Running pagurus as a wrapper for a single user

# Start running wrapper in the background for username
pagurus -u $USER -mv -p /path/to/output/dir -o test.csv
# Get the previous running PID of pagurus
export PID=$!
# Sleep for a few seconds to let everything start running
sleep 10 

###########################

# Run your desired program as normal
./a.out

# Works with containers
shifter --image=tylern4/memoryhog:latest alloc 2

# and with wrapper scripts
shifter --image=jfroula/aligner-bbmap:2.0.2 bbmap.sh Xmx12g in=sample.fastq.bz2 ref=sample.fasta out=test.sam

###########################

# Kill the pagurus process
kill $PID

# Sleep for a few seconds to let results finish writing
sleep 10